Question: msnbase error when adding identification data
0
gravatar for queso012
4.4 years ago by
queso0120
United States
queso0120 wrote:

Hi,

I'm trying to msnbase to process my itraq data. I'm getting an error message when I try to add identification data. Please see my code and error message below. My raw data input is mzXML files  (.raw converted to mzXML using Proteowizard) and my mzIdent files are from Mascot.

files=dir("/Users/kasojimd/Projects/ccrifx-541/Raw2mzXML",full.names=T,patter="mzXML")

rawdata=readMSData(files)

identFile=list.files(pattern=".mzid$")

msexp <- addIdentificationData(rawdata, filenames = identFile, verbose = FALSE)
Error in basename(id$spectrumFile) : a character vector argument expected

Any suggestions on how to get past this will be appreciated! I am new to proteomics data, so any other bioconductor package option suggestions will be appreciated too. I have already tried isobar, however I have come across  much difficulty when trying to use it.

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] MSnbase_1.12.1       mzR_1.10.8           Rcpp_0.11.3          ggplot2_1.0.0        BiocInstaller_1.14.3 isobar_1.10.0       
[7] plyr_1.8.1           Biobase_2.24.0       BiocGenerics_0.10.0 

loaded via a namespace (and not attached):
 [1] affy_1.42.3              affyio_1.32.0            codetools_0.2-9          colorspace_1.2-4         digest_0.6.8            
 [6] distr_2.5.3              doParallel_1.0.8         foreach_1.4.2            grid_3.1.0               gtable_0.1.2            
[11] impute_1.38.1            IRanges_1.22.10          iterators_1.0.7          labeling_0.3             lattice_0.20-29         
[16] limma_3.20.9             MASS_7.3-37              munsell_0.4.2            mzID_1.2.1               pcaMethods_1.54.0       
[21] preprocessCore_1.26.1    proto_0.3-10             reshape2_1.4.1           scales_0.2.4             sfsmisc_1.0-27          
[26] startupmsg_0.9           stats4_3.1.0             stringr_0.6.2            SweaveListingUtils_0.6.2 tools_3.1.0             
[31] vsn_3.32.0               XML_3.98-1.1             zlibbioc_1.10.0         

 

proteomics itraq msnbase • 1.2k views
ADD COMMENTlink modified 4.4 years ago by Laurent Gatto1.1k • written 4.4 years ago by queso0120

Also, I have already taken a look at the thread posted here regarding the issue. It seems to not be resolved yet:

https://github.com/lgatto/MSnbase/issues/39

ADD REPLYlink written 4.4 years ago by queso0120
Answer: msnbase error when adding identification data
0
gravatar for Laurent Gatto
4.4 years ago by
Laurent Gatto1.1k
United Kingdom
Laurent Gatto1.1k wrote:

I think your should not have this error any more with a recent version of MSnbase. From the NEWS file, I can see

CHANGES IN VERSION 1.15.1
-------------------------
 o Fixing error when id file has no spectrumFile info (see issue #39)
   and return a warning (instead of an error) when the file used to
   create the MSnExp/MSnSet and mzid file were different
   [2014-10-15 Wed]

However, this corresponds to the current development version. There are several options:

  1. You install the development version of R, which will get you the Bioc devel and MSnbase 1.15.3. Beforehand, feel free to share the data with me and I will test it for you. I might actually even be possible (without guarantee, however) for you to continue with the object I create on your system.
  2. You use the bioconductor/devel_proteomics docker container to get up and running with devel in no time without messing up with your current installation.
  3. (I port the fix to release, but that will require some time.)

Option 2 is the fastest for you. Option 1 will take a bit of time.

Your is the previous stable version, so I would suggest you update anyway.

Laurent
 

ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by Laurent Gatto1.1k
1

More info about using Bioconductor in Docker is here.

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by Dan Tenenbaum8.2k

Thanks, Dan, I forgot to add the link.

ADD REPLYlink written 4.4 years ago by Laurent Gatto1.1k

Thanks for the solutions! I was able to successfully install boot2docker for mac, run bioconductor/devel_base R and install and load MSnbase. However, I cannot access my local drive ( I cannot set the working directory). Any suggestions on how to accomplish this? 

ADD REPLYlink written 4.4 years ago by queso0120
See https://github.com/rocker-org/rocker/wiki/Sharing-files-with-host-machine On January 15, 2015 6:08:27 PM PST, "queso012 [bioc]" <noreply@bioconductor.org> wrote: >queso012 posted the Comment: "msnbase error when adding identification >data": > >Thanks for the solutions! I was able to successfully install >boot2docker for mac, run bioconductor/devel_base R and install and load >MSnbase. However, I cannot access my local drive ( I cannot set the >working directory). Any suggestions on how to accomplish this? > >--- >See the full post at: C: msnbase error when adding identification data >Replying to this email will post a comment to the answer above.
ADD REPLYlink written 4.4 years ago by Dan Tenenbaum8.2k
See https://github.com/rocker-org/rocker/wiki/Sharing-files-with-host-machine On January 15, 2015 6:08:27 PM PST, "queso012 [bioc]" <noreply@bioconductor.org> wrote: >queso012 posted the Comment: "msnbase error when adding identification >data": > >Thanks for the solutions! I was able to successfully install >boot2docker for mac, run bioconductor/devel_base R and install and load >MSnbase. However, I cannot access my local drive ( I cannot set the >working directory). Any suggestions on how to accomplish this? > >--- >See the full post at: C: msnbase error when adding identification data >Replying to this email will post a comment to the answer above.
ADD REPLYlink written 4.4 years ago by Dan Tenenbaum8.2k

Thanks -- I was able to successfully connect, however I still receive an error at the addition of the identification step:

> msexp <- addIdentificationData(rawdata, filenames = identFile, verbose = FALSE)

Error in basename(id$spectrumFile) : a character vector argument expected

> sessionInfo()

R version 3.1.0 (2014-04-10)

Platform: x86_64-apple-darwin13.1.0 (64-bit)

 

locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

 

attached base packages:

[1] parallel  stats     graphics  grDevices utils     datasets  methods  

[8] base     

 

other attached packages:

[1] MSnbase_1.12.1      mzR_1.10.8          Rcpp_0.11.3        

[4] ggplot2_1.0.0       Biobase_2.24.0      BiocGenerics_0.10.0

 

loaded via a namespace (and not attached):

 [1] affy_1.42.3           affyio_1.32.0         BiocInstaller_1.14.3 

 [4] codetools_0.2-9       colorspace_1.2-4      digest_0.6.8         

 [7] doParallel_1.0.8      foreach_1.4.2         grid_3.1.0           

[10] gtable_0.1.2          impute_1.38.1         IRanges_1.22.10      

[13] iterators_1.0.7       lattice_0.20-29       limma_3.20.9         

[16] MASS_7.3-37           munsell_0.4.2         mzID_1.2.1           

[19] pcaMethods_1.54.0     plyr_1.8.1            preprocessCore_1.26.1

[22] proto_0.3-10          reshape2_1.4.1        scales_0.2.4         

[25] stats4_3.1.0          stringr_0.6.2         vsn_3.32.0           

[28] XML_3.98-1.1          zlibbioc_1.10.0      

ADD REPLYlink written 4.4 years ago by queso0120

As far as I can see, this still uses R version 3.1.0 and MSnbase 1.12.1.

ADD REPLYlink written 4.4 years ago by Laurent Gatto1.1k
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